Unix and Perl Primer for Biologists

Keith Bradnam & Ian Korf

http://korflab.ucdavis.edu/Unix_and_Perl/

EDIT: Go look at Pierre's answer.

I don't think you'll need a bash tutorial tailored to biologists. If you've worked on a Mac or a PC, try doing your everyday stuff without a mouse, on a terminal. That'll set you on the right path.

Besides coreutils (such as mkdir, cd, cp, mv, rm, ls, etc), you'll find cut, sort, uniq, tr and find really useful. And the three core text processing utilities - grep, sed and awk - will revolutionarize the way you think of a Search/Replace operation on text editors.

You'll also have to learn pipes, to get a series of tasks done, and redirection, to read from and write to files.

Learn the $(command) syntax to store the output of commands in variables. Once done, move on to loops using variables and then loops that use output from commands. In parallel, also focus on the differences between the single, double and back quotes.

But, bash has so many options that unless you use these frequently, you'll forget them. And then, like all of us, you'll run man command_name and re-learn them in a minute.

Oh, and to conclude: https://xkcd.com/1168/